LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-345-g506bf886ee-modified)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
# 2d micelle simulation

dimension	2

neighbor	0.3 bin
neigh_modify	delay 5

atom_style	bond

# Soft potential push-off

read_data	data.micelle
Reading data file ...
  orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  1200 atoms
  scanning bonds ...
  1 = max bonds/atom
  reading bonds ...
  300 bonds
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.004 seconds
special_bonds	fene
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
     2 = max # of 1-2 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds

pair_style	soft 1.12246
pair_coeff	* * 0.0 1.12246

bond_style 	harmonic
bond_coeff	1 50.0 0.75

velocity	all create 0.45 2349852

variable	prefactor equal ramp(1.0,20.0)

fix		1 all nve
fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix		3 all adapt 1 pair soft a * * v_prefactor
fix		4 all enforce2d

thermo		50
run		500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730)
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.42246
  ghost atom cutoff = 1.42246
  binsize = 0.71123, bins = 51 51 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair soft, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/2d
      bin: standard
WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730)
Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0.45           0.40003481     2.2200223e-06  0.84966203     0.78952518   
        50   0.54981866     0.93548899     0.068440043    1.5532895      1.9232786    
       100   0.45           0.99659327     0.079228519    1.5254468      3.2135679    
       150   0.86965411     0.90456016     0.07493355     1.8484231      4.3821925    
       200   0.45           1.01454        0.10663502     1.5708         4.7598476    
       250   0.79636561     0.82567712     0.12105337     1.7424325      5.4983899    
       300   0.45           0.86475538     0.11819875     1.4325791      5.8554758    
       350   0.72135464     0.70693069     0.10912636     1.5368106      6.0388247    
       400   0.45           0.75067331     0.14165013     1.3419484      6.3840708    
       450   0.64839221     0.62402486     0.14173679     1.4136135      6.4791009    
       500   0.45           0.66669513     0.13695201     1.2532721      6.807146     
Loop time of 0.0138659 on 4 procs for 500 steps with 1200 atoms

Performance: 15577811.312 tau/day, 36059.748 timesteps/s, 43.272 Matom-step/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0053896  | 0.0057144  | 0.0060899  |   0.4 | 41.21
Bond    | 0.00020074 | 0.00021422 | 0.00022291 |   0.0 |  1.54
Neigh   | 0.0025301  | 0.0025401  | 0.0025501  |   0.0 | 18.32
Comm    | 0.0031194  | 0.0035074  | 0.0038196  |   0.4 | 25.30
Output  | 6.4137e-05 | 6.7743e-05 | 7.7909e-05 |   0.0 |  0.49
Modify  | 0.0013391  | 0.0013582  | 0.0013972  |   0.1 |  9.80
Other   |            | 0.0004638  |            |       |  3.34

Nlocal:            300 ave         304 max         292 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Nghost:          103.5 ave         108 max          98 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs:          773.5 ave         792 max         735 min
Histogram: 1 0 0 0 0 0 0 0 2 1

Total # of neighbors = 3094
Ave neighs/atom = 2.5783333
Ave special neighs/atom = 0.5
Neighbor list builds = 52
Dangerous builds = 0

unfix		3

# Main run

pair_style	lj/cut 2.5

# solvent/head - full-size and long-range

pair_coeff	1 1 1.0 1.0 2.5
pair_coeff	2 2 1.0 1.0 2.5
pair_coeff	1 2 1.0 1.0 2.5

# tail/tail - size-averaged and long-range

pair_coeff	3 3 1.0 0.75 2.5
pair_coeff	4 4 1.0 0.50 2.5
pair_coeff	3 4 1.0 0.67 2.5

# solvent/tail - full-size and repulsive

pair_coeff	1 3 1.0 1.0 1.12246
pair_coeff	1 4 1.0 1.0 1.12246

# head/tail - size-averaged and repulsive

pair_coeff	2 3 1.0 0.88 1.12246
pair_coeff	2 4 1.0 0.75 1.12246

thermo		50

#dump		1 all atom 2000 dump.micelle

#dump		2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75

#dump		3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75

reset_timestep	0
group solvent   molecule 0
750 atoms in group solvent
group solute    subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix		1 solvent nve
fix		2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix		5 solute rigid molecule langevin 0.45 0.45 0.5 112211
  150 rigid bodies with 450 atoms
fix		4 all enforce2d
run		500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 26 26 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.375 | 5.375 | 5.375 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0.45318168    -1.3753652      0.13695201    -0.8705807      1.975423     
        50   0.77344732    -1.6944083      0.13695201    -0.92967487     0.58657109   
       100   0.53530681    -1.7006195      0.13695201    -1.1291768      0.11219772   
       150   0.60820175    -1.8071581      0.13695201    -1.176549       1.5161796    
       200   0.49410558    -1.7945459      0.13695201    -1.2565449      4.0469262    
       250   0.52460847    -1.8528672      0.13695201    -1.290108       2.9929445    
       300   0.46596803    -1.8680499      0.13695201    -1.3528872      2.7958851    
       350   0.48831812    -1.8723486      0.13695201    -1.3390451     -4.5106818    
       400   0.46798432    -1.9008529      0.13695201    -1.3840536     -4.3096566    
       450   0.46000658    -1.9081144      0.13695201    -1.3977904      3.3360611    
       500   0.45822409    -1.9077531      0.13695201    -1.3988759      0.45428738   
Loop time of 0.0381773 on 4 procs for 500 steps with 1200 atoms

Performance: 5657810.772 tau/day, 13096.784 timesteps/s, 15.716 Matom-step/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0059651  | 0.0062314  | 0.0066404  |   0.3 | 16.32
Bond    | 0.00021057 | 0.00022477 | 0.0002333  |   0.0 |  0.59
Neigh   | 0.0041424  | 0.0041487  | 0.0041512  |   0.0 | 10.87
Comm    | 0.004264   | 0.0047244  | 0.0050297  |   0.4 | 12.37
Output  | 8.2396e-05 | 8.6559e-05 | 9.6749e-05 |   0.0 |  0.23
Modify  | 0.021833   | 0.021946   | 0.022094   |   0.1 | 57.48
Other   |            | 0.0008157  |            |       |  2.14

Nlocal:            300 ave         303 max         296 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost:         216.25 ave         219 max         214 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs:        2189.75 ave        2205 max        2173 min
Histogram: 1 0 0 0 1 0 1 0 0 1

Total # of neighbors = 8759
Ave neighs/atom = 7.2991667
Ave special neighs/atom = 0.5
Neighbor list builds = 46
Dangerous builds = 2
unfix 2
unfix 4
unfix 5
fix		5 solute rigid/small molecule
  create bodies CPU = 0.000 seconds
  150 rigid bodies with 450 atoms
  1.3043524 = max distance from body owner to body atom
fix		4 all enforce2d
run		500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.233 | 9.233 | 9.234 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
       500   0.45822409    -1.9077531      0.13695201    -1.3988759      2.4509752    
       550   0.46736204    -1.9141964      0.13695201    -1.3979022      2.1695662    
       600   0.47872194    -1.9232781      0.13695201    -1.3977635      2.0058379    
       650   0.47491575    -1.9224109      0.13695201    -1.3999857      2.0637789    
       700   0.44714331    -1.8990682      0.13695201    -1.3991848      2.4863082    
       750   0.49089274    -1.9231004      0.13695201    -1.3877071      2.123147     
       800   0.4753839     -1.8959698      0.13695201    -1.3731645      2.3030481    
       850   0.46870816    -1.8972225      0.13695201    -1.3798357      2.2464703    
       900   0.49610454    -1.9070748      0.13695201    -1.3674513      2.2196388    
       950   0.4773035     -1.8925765      0.13695201    -1.3682132      2.3534786    
      1000   0.50413702    -1.9292393      0.13695201    -1.383096       2.1630987    
Loop time of 0.0236819 on 4 procs for 500 steps with 1200 atoms

Performance: 9120883.727 tau/day, 21113.157 timesteps/s, 25.336 Matom-step/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0058656  | 0.0059718  | 0.0061355  |   0.1 | 25.22
Bond    | 0.0002083  | 0.00022447 | 0.00023485 |   0.0 |  0.95
Neigh   | 0.0035477  | 0.0035644  | 0.0035824  |   0.0 | 15.05
Comm    | 0.0041037  | 0.0042227  | 0.0043024  |   0.1 | 17.83
Output  | 7.4355e-05 | 7.8273e-05 | 8.7777e-05 |   0.0 |  0.33
Modify  | 0.008976   | 0.0090549  | 0.0091663  |   0.1 | 38.24
Other   |            | 0.0005654  |            |       |  2.39

Nlocal:            300 ave         306 max         295 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost:            221 ave         226 max         217 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs:         2163.5 ave        2271 max        2100 min
Histogram: 1 1 0 1 0 0 0 0 0 1

Total # of neighbors = 8654
Ave neighs/atom = 7.2116667
Ave special neighs/atom = 0.5
Neighbor list builds = 39
Dangerous builds = 0
Total wall time: 0:00:00
